(623b) DNA CpG Methylation Patterns Distinctively Modulate Chromatin Structure

DNA CpG methylation plays a key role in gene regulation. It induces compaction of the chromatin fiber and leads to gene silencing. DNA methylation is a potential biomarker for early detection of cancer since abnormal DNA methylation patterns have been observed in the promoter regions of tumor suppressor genes in early stages of tumorigenesis. Therefore, it is critical to understand the underlying mechanism as to how DNA methylation directly modulates chromatin structure and gene expression. In this study, we constructed chromatin-like molecules, i.e. nucleosomes and nucleosome arrays, containing defined unmethylated and methylated CpG patterns. Using various biophysical assays, we elucidated how different CpG patterns and methylation levels can modulate chromosome dynamics and conformation. Unmethylated CpG dinucleotides at 10bp intervals induced a more open nucleosome conformation. In addition, when in contact with the histone proteins, this CpG pattern destabilized the nucleosome structure. As we increased the DNA methylation level to 100%, we found that methylated CpG dinucleotides can distinctively alter nucleosome and nucleosome array conformation, depending on their relative positions within the nucleosomal DNA. A more open conformation was observed in nucleosomes with a stretch of methylated CpG dinucleotides in the central dyad. The opposite effect was found when the methylated CpG dinucleotides were located at 10bp intervals.  In the case of nucleosome arrays, DNA methylation had a different effect on array conformation depending on the position of the CpG sites.  These observations give us molecular insights into the regulatory mechanisms of gene expression driven by DNA methylation. In addition, identifying CpG patterns that are important for modulation of chromosome structure associated with DNA methylation is instrumental in the identification of relevant DNA methylation biomarkers for cancer.